
#######################################################
#                                                     #
#                        LGA                          #
#                  ---------------                    #
#                                                     #
#               Local-Global Alignment                #
#        A Method for Finding 3-D Similarities        #
#               in Protein Structures                 #
#                                                     #
#                  ------------ 10/2009               #
#                                                     #
#      Adam Zemla (adamz@llnl.gov)                    #
#      Lawrence Livermore National Laboratory, CA     #
#                                                     #
#######################################################

!!!   License for LGA program has expired  !!!
#   For updated version of the LGA program   #
# please contact Adam Zemla:  adamz@llnl.gov #

# Molecule1: number of CA atoms   48 (  393),  selected   48 , name one
# Molecule2: number of CA atoms   97 (  780),  selected   48 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:A  -ch2:A  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    48      52_A - 99_A        0.56     0.56
  LCS_AVERAGE:     49.48

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    48      52_A - 99_A        0.56     0.56
  LCS_AVERAGE:     49.48

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    48      52_A - 99_A        0.56     0.56
  LCS_AVERAGE:     49.48

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   48
LCS_GDT     RESIDUE       RESIDUE       SEGMENT_SIZE    GLOBAL DISTANCE TEST COLUMNS: number of residues under the threshold assigned to each residue pair
LCS_GDT   NAME NUMBER   NAME NUMBER    1.0  2.0  5.0    0.5  1.0  1.5  2.0  2.5  3.0  3.5  4.0  4.5  5.0  5.5  6.0  6.5  7.0  7.5  8.0  8.5  9.0  9.5 10.0
LCS_GDT     G    52_A     G    52_A     48   48   48     10   35   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     E    53_A     E    53_A     48   48   48      4   44   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     W    54_A     W    54_A     48   48   48     38   45   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     E    55_A     E    55_A     48   48   48     38   45   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     I    56_A     I    56_A     48   48   48     38   45   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     I    57_A     I    57_A     48   48   48     38   45   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     D    58_A     D    58_A     48   48   48     38   45   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     I    59_A     I    59_A     48   48   48     38   45   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     G    60_A     G    60_A     48   48   48     38   45   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     P    61_A     P    61_A     48   48   48     38   45   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     F    62_A     F    62_A     48   48   48     38   45   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     T    63_A     T    63_A     48   48   48     38   45   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     Q    64_A     Q    64_A     48   48   48     38   45   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     N    65_A     N    65_A     48   48   48     38   45   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     L    66_A     L    66_A     48   48   48     38   45   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     G    67_A     G    67_A     48   48   48     38   45   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     K    68_A     K    68_A     48   48   48     38   45   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     F    69_A     F    69_A     48   48   48     38   45   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     A    70_A     A    70_A     48   48   48     38   45   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     V    71_A     V    71_A     48   48   48     38   45   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     D    72_A     D    72_A     48   48   48     38   45   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     E    73_A     E    73_A     48   48   48     38   45   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     E    74_A     E    74_A     48   48   48     38   45   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     N    75_A     N    75_A     48   48   48     38   45   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     K    76_A     K    76_A     48   48   48     38   45   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     I    77_A     I    77_A     48   48   48     38   45   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     G    78_A     G    78_A     48   48   48     23   45   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     Q    79_A     Q    79_A     48   48   48     23   45   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     Y    80_A     Y    80_A     48   48   48     38   45   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     G    81_A     G    81_A     48   48   48     38   45   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     R    82_A     R    82_A     48   48   48     38   45   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     L    83_A     L    83_A     48   48   48     38   45   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     T    84_A     T    84_A     48   48   48     38   45   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     F    85_A     F    85_A     48   48   48     38   45   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     N    86_A     N    86_A     48   48   48     38   45   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     K    87_A     K    87_A     48   48   48     38   45   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     V    88_A     V    88_A     48   48   48     38   45   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     I    89_A     I    89_A     48   48   48     38   45   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     R    90_A     R    90_A     48   48   48     38   45   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     P    91_A     P    91_A     48   48   48     38   45   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     C    92_A     C    92_A     48   48   48     38   45   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     M    93_A     M    93_A     48   48   48     34   45   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     K    94_A     K    94_A     48   48   48     38   45   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     K    95_A     K    95_A     48   48   48     22   45   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     T    96_A     T    96_A     48   48   48     23   45   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     I    97_A     I    97_A     48   48   48      5   45   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     Y    98_A     Y    98_A     48   48   48      5   45   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     E    99_A     E    99_A     48   48   48      5   32   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_AVERAGE  LCS_A:  49.48  (  49.48   49.48   49.48 )

GLOBAL_DISTANCE_TEST (summary information about detected largest sets of residues (represented by selected AToms) that can fit under specified thresholds)
GDT DIST_CUTOFF  0.50   1.00   1.50   2.00   2.50   3.00   3.50   4.00   4.50   5.00   5.50   6.00   6.50   7.00   7.50   8.00   8.50   9.00   9.50  10.00
GDT NUMBER_AT     38     45     47     48     48     48     48     48     48     48     48     48     48     48     48     48     48     48     48     48 
GDT PERCENT_AT  39.18  46.39  48.45  49.48  49.48  49.48  49.48  49.48  49.48  49.48  49.48  49.48  49.48  49.48  49.48  49.48  49.48  49.48  49.48  49.48
GDT RMS_LOCAL    0.30   0.44   0.50   0.56   0.56   0.56   0.56   0.56   0.56   0.56   0.56   0.56   0.56   0.56   0.56   0.56   0.56   0.56   0.56   0.56
GDT RMS_ALL_AT   0.62   0.56   0.56   0.56   0.56   0.56   0.56   0.56   0.56   0.56   0.56   0.56   0.56   0.56   0.56   0.56   0.56   0.56   0.56   0.56

# Checking swapping
#   possible swapping detected:  E    55_A      E    55_A
#   possible swapping detected:  F    69_A      F    69_A
#   possible swapping detected:  E    73_A      E    73_A
#   possible swapping detected:  E    74_A      E    74_A
#   possible swapping detected:  F    85_A      F    85_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    G    52_A      G    52_A     1.695     0    0.035   0.035     2.055   75.119   75.119
LGA    E    53_A      E    53_A     1.163     0    0.073   0.848     4.350   85.952   70.265
LGA    W    54_A      W    54_A     0.615     0    0.065   0.098     1.113   88.214   90.510
LGA    E    55_A      E    55_A     0.383     0    0.058   1.013     4.628   97.619   76.138
LGA    I    56_A      I    56_A     0.313     0    0.026   0.619     2.588  100.000   94.643
LGA    I    57_A      I    57_A     0.338     0    0.041   0.082     0.477  100.000  100.000
LGA    D    58_A      D    58_A     0.310     0    0.075   0.560     2.135  100.000   93.214
LGA    I    59_A      I    59_A     0.434     0    0.054   0.113     0.465  100.000  100.000
LGA    G    60_A      G    60_A     0.266     0    0.042   0.042     0.324  100.000  100.000
LGA    P    61_A      P    61_A     0.408     0    0.024   0.034     0.533  100.000   98.639
LGA    F    62_A      F    62_A     0.533     0    0.041   0.162     0.878   97.619   93.074
LGA    T    63_A      T    63_A     0.419     0    0.012   1.068     2.192  100.000   89.728
LGA    Q    64_A      Q    64_A     0.198     0    0.012   0.081     0.334  100.000  100.000
LGA    N    65_A      N    65_A     0.461     0    0.072   0.217     1.049  100.000   94.107
LGA    L    66_A      L    66_A     0.417     0    0.027   0.256     0.537  100.000   98.810
LGA    G    67_A      G    67_A     0.101     0    0.016   0.016     0.227  100.000  100.000
LGA    K    68_A      K    68_A     0.135     0    0.050   1.398     6.902  100.000   73.439
LGA    F    69_A      F    69_A     0.291     0    0.015   0.095     0.709  100.000   97.403
LGA    A    70_A      A    70_A     0.219     0    0.023   0.036     0.285  100.000  100.000
LGA    V    71_A      V    71_A     0.148     0    0.017   0.067     0.321  100.000  100.000
LGA    D    72_A      D    72_A     0.303     0    0.018   0.059     0.484  100.000  100.000
LGA    E    73_A      E    73_A     0.391     0    0.036   0.107     0.516  100.000   98.942
LGA    E    74_A      E    74_A     0.387     0    0.045   0.192     0.434  100.000  100.000
LGA    N    75_A      N    75_A     0.176     0    0.027   0.102     0.539  100.000   98.810
LGA    K    76_A      K    76_A     0.119     0    0.022   0.122     0.390  100.000  100.000
LGA    I    77_A      I    77_A     0.227     0    0.008   0.122     0.526  100.000   98.810
LGA    G    78_A      G    78_A     0.585     0    0.027   0.027     0.690   92.857   92.857
LGA    Q    79_A      Q    79_A     0.725     0    0.013   0.946     4.576   90.476   76.349
LGA    Y    80_A      Y    80_A     0.481     0    0.018   0.052     1.034   95.238   91.310
LGA    G    81_A      G    81_A     0.524     0    0.031   0.031     0.524   97.619   97.619
LGA    R    82_A      R    82_A     0.394     0    0.106   1.129     5.486   97.619   78.961
LGA    L    83_A      L    83_A     0.177     0    0.018   0.144     0.560  100.000   98.810
LGA    T    84_A      T    84_A     0.300     0    0.071   0.121     0.464  100.000  100.000
LGA    F    85_A      F    85_A     0.303     0    0.008   0.050     0.409  100.000  100.000
LGA    N    86_A      N    86_A     0.315     0    0.020   0.909     2.059  100.000   92.202
LGA    K    87_A      K    87_A     0.352     0    0.040   0.108     0.393  100.000  100.000
LGA    V    88_A      V    88_A     0.364     0    0.023   0.059     0.448  100.000  100.000
LGA    I    89_A      I    89_A     0.290     0    0.018   0.052     0.430  100.000  100.000
LGA    R    90_A      R    90_A     0.411     0    0.033   0.947     4.587   95.238   80.173
LGA    P    91_A      P    91_A     0.331     0    0.040   0.068     0.645  100.000   98.639
LGA    C    92_A      C    92_A     0.194     0    0.083   0.128     0.509   97.619   98.413
LGA    M    93_A      M    93_A     0.614     0    0.022   0.990     4.600   95.238   84.345
LGA    K    94_A      K    94_A     0.320     0    0.109   0.630     3.630   97.619   81.270
LGA    K    95_A      K    95_A     0.836     0    0.027   0.576     1.343   90.476   87.460
LGA    T    96_A      T    96_A     0.563     0    0.019   0.087     1.380   92.857   90.544
LGA    I    97_A      I    97_A     0.960     0    0.057   0.372     1.717   90.476   83.810
LGA    Y    98_A      Y    98_A     1.078     0    0.035   0.102     1.663   79.286   82.222
LGA    E    99_A      E    99_A     1.360     0    0.033   0.787     3.037   77.143   67.937

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       48     192    192  100.00     393    393  100.00                97
SUMMARY(RMSD_GDC):     0.558          0.564                  1.167           47.776   45.614

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   48   97    4.0     48    0.56    48.711    49.164     7.290

LGA_LOCAL      RMSD:   0.558  Number of atoms:   48  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.558  Number of assigned atoms:   48 
Std_ASGN_ATOMS RMSD:   0.558  Standard rmsd on all 48 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.130690 * X  +   0.976357 * Y  +  -0.172182 * Z  +  -4.262960
  Y_new =  -0.950449 * X  +   0.172797 * Y  +   0.258434 * Z  +  11.394254
  Z_new =   0.282076 * X  +   0.129875 * Y  +   0.950561 * Z  +  45.094147 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.434150 -0.285958  0.135789   [DEG:  -82.1707  -16.3842    7.7802 ]
ZXZ: -2.553878  0.315760  1.139306   [DEG: -146.3264   18.0917   65.2774 ]
 
# END of job
